The failure to deal with the emotional and psychic damage that was done to so many in the crew is one of the reasons I despise the "cliffhanger" in "Zero Hour" and the subsequent time-waster "Stormfront" -- parts one and two no less.

So much happened in S3, "Home" could easily have been a 2-3 parter:
-- Archer's guilt over stranding the aliens. His regrets over the death of Degra.
-- T'Pol mainlining trellium.
-- Hoshi being tortured (can you say post-traumatic stress?).
-- Phlox violating the Lysarrian protocols to create Sim (and then murdering him to save Trip). I'm thinking the Lyssarians might be kind of annoyed about that. And we never do find out how Tucker felt about that, either.
-- Reed (on Archer's orders) kills 3 people when he fires without warning on a Xindi communication station.
-- The Imperial Guard must have been thrilled when Shran blew his mission to take the prototype planet buster.
-- Humanity's xenophobia that got its only airing in a bar fight. And where is the resentment of the Vulcans who did nothing to help defend Earth during the second attack?
-- Trip comes home from the mission and we still don't get to see his family.
I 100% agree with everything you stated. More needed to be addressed to fully put into scope one incident (the piracy) as a series of other major incidents that impacted different crew members in different ways.)) I took the easy way out by just staying in the Archer box.
Stormfront did nothing to address what happened to the crew as a whole, and as individuals, and Home was woefully inadequate in dealing with the sheer magnitude of stresses put upon each person on the NX-01 throughout that mission. These people had been thru so much, that by the end of zero hour, they deserved to get home (yeah, life's not always fair, or well written) - and gotten to the business of healing - not to a tired set-up involving alien nazi's and all the inconsistencies there... If I were on the NX-01 - I think I would've done an equal double take to what most of the viewers did - it made no sense whatsoever (and I still want to know why the Aquatic vessel would leave Enterprise without realizing and assisting them knowing the stars were out of alignment and they were all 200 years in the past-give or take. They surely knew in E2 when they were that far out of sync in the flashback to their exiting that wormhole.) Yeah - they had to wrap up that wonderful story device called the temporal cold war some way or some how, but .......... I'll stop... Sorry for the rambling. I'll get back OT.
Off your list, JINX, the one's that hit me the hardest at first read:
#1 - Not adequately dealing with T-Pol's trellium addiction was a huge missed opportunity and an unforgivable story telling exclusion IMHO (I will never forget watching the end of Azati Prime and seeing the "high" t'pol in command of the NX-01 as it's getting pounded. Her mouth was shut and she's staring off into the fires that had broken out on the bridge. Arguably in her mind, maybe she thought they were toast by then, but what about going down fighting? No orders, no nothing. I realize we didn't know, for sure, yet (as viewers, we get the luxury of looking at it in retrospect - watching Damage and then realizing we had a drug addicted captain in Azati Prime during the show's worst battle) about her emotional problems and their cause - therefore - wouldn't it have been strong story to look at her drug influenced actions and deal with how they impacted both her personal relationships (not just with Trip) and command decisions. You never just 'get away' from such a bad drug addiction as she was saddled with and have as little repercussions as she did. Yes - she had emotions she now had to more fully acknowledge, but recovery is a bi*ch, and yes, your friends and shipmates of 3 years would notice the downhill spiral, the rock bottom, and the climb to recovery. Phlox's magic 3 day relief elixer from the shakes and the physical toll that stuff took on her was a cop out. We all know, from the much more realistic portrayals of drug addiction on other shows, what the sequence of events is (or, if you've had to deal with it in your own life in some way, either as an observer or the person who's addicted) But, we did get to continually putting Trip thru the ringer - carrying on the relation that arguably started because of the drugs to begin with... Yeah,
we knew what was happening, but the characters never got to turn the tables on T'Pol and confront her in any way.
#2 - Hoshi's dual torture at the hands of Dolim (Dolum?) and then the degree to which Archer pushed and pushed her as the mission became critical. (Archer needed her skills, but, man, Hoshi got emotionally burnt twice back to back.) When she got "home" I didn't expect her to have the parasites removed, get a smile from Dr. Phlox, and then go about getting some Madame Changs (and us, as viewers, see nothing related to what that woman went thru beyond that.) If she survived both those incidents with as little ramifications as she did - hat's off to Hoshi - until 10 years later when it all comes back because of some other trigger.
I guess Hoshi didn't warrant the screen time to explore the awful nightmares, waking fears, etc. she had to have been going thru.
#3 - Trip never having the opportunity to show, on screen, his reactions to Sim and his creaton - to save his own life. Not to mention to contemplate what Phlox and Archer went thru by making the decision in the first place. I just wrote about this in another thread, so I won't do more here, but another missed opportunity.
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Sorry about my mistake regarding Archer saying he'd go back for the stranded ship - I must've had hoped that Archer would've put them on his list of things to do when ENT was safe - so I suppose I imagined those lines of dialogue. Though, as Bak_and_Blue stated, after thinking about it, IF they would've addressed what you posited, gblews, thru strong writing, not just a couple sexual encounters with Captain Hernandez, I very much like your scenario better. When they got to "Home"- they/we should've been afforded a 3 episode arc, in my opinion, and really got down to some serious exploring - - of our characters and what all that time in the expanse did to them. Shame there's virtually nothing for Travis to explore along with them. Shran's got more than Travis to dig into - story wise.